Journal:Acta Cryst F:S2053230X20002988

Structural characterization of the human O-phosphoethanolamine phospho-lyase

Chiara Vettraino, Alessio Peracchi, Stefano Donini, Emilio Parisini ^[1]

Molecular Tour
The human O-phosphoethanolamine phospho-lyase (hEtnppl) is an enzyme dependent on pyridoxal 5'-phosphate (PLP) that catalyzes the degradation of O-phosphoethanolamine (PEA) into acetaldehyde, phosphate and ammonia. Physiologically, the enzyme is involved in the phospholipid metabolism, since PEA is the precursor of phosphatidylethanolamine (PE), one of the four main membrane phospholipids, in the CDP-ethanolamine-Kennedy pathway. Indeed, it has been demonstrated that the knock-down of hEtnppl disrupts the normal synthesis of lipids in Hepatocellular carcinoma (HCC) and Cholangiocellular carcinoma (CCA) tissues, promoting an unusual activated lipogenesis (called de novo lipogenesis, DNL) that plays an essential role in supplying phospholipids during tumorigenesis. Moreover, the expression of the enzyme has been shown to decrease both in ovarian cancer and in breast cancer tissues and to increase in neuropsychiatric diseases such as schizophrenia and bipolar disorder. This enzyme was originally named AGXT2L1 (AGXT2-like 1) based on its homology to alanine glyoxylate aminotransferase 2 (AGXT2), a mitochondrial PLP-dependent enzyme that transaminates a variety of substrates while also acting as a lyase on L-cysteine conjugates. Unlike AGXT2, however, hEtnppl is almost completely inactive as a transaminase. Instead, it was shown to catalyze the irreversible 1,2-elimination of O-phosphophenanolamine (PEA) to produce acetaldehyde, phosphate and ammonia.

Overall structure of the PMP-bound form of hEtnppl (PDB entry 6tor):

• . Chains A, and B are colored in blue and cyan, respectively. The bound PMP molecule is represented as grey stick.
• Although you may explore and rotate every structure with the mouse, here you can see a .

. The N-terminal lobe (residues 1-85), large domain (residues 86-301) and C-terminal lobe (residues 302-499) are colored in cyan, magenta and green, respectively.

Dimer interface in the hEtnppl structure (spacefill representation of the dimer subunits):

• . The critically important residues forming interface contacts are colored in blue (chain A) and cyan (chain B).
• Although you may explore and rotate every structure with the mouse, here you can see a .

are labeled. Hydrogen bonds are indicated by dashed lines.

The crystal structure of hEtnppl (determined at 2.05 Å resolution) shows high similarity to the crystal structure of the phospho-lyase A1RDF1 from Arthrobacter aurescens TC1, which so far has been the only phospho-lyase structure reported in the literature. The active site of hEtnppl is located at the interface between the two subunits of the dimer, each subunit making crucial contributions to the active site. Most of the residues that line the catalytic pocket correspond to those found in the close structural homolog A1RDF1, strongly suggesting that these enzymes share a common mechanism. While confirming the presence of a cluster of positively charged residues for the recognition of the phosphate moiety of the substrate, the structure of the active site of hEtnppl suggests a striking mobility of the crucial catalytic residue K278. In hEtnppl, the cofactor binds essentially in the same position as in A1RDF1 in complex with and [key residues of hEtnppl (green) and A1RDF1 (white) active site, and molecule bound are presented in ball-and-sticks, and are numbered in the corresponding color. Residue from the opposite monomer are marked (*). Water molecules are shown as red spheres]. However, in the crystal structure of hEtnppl, the cofactor does not covalently bind the ε-amino group of the adjacent K278 residue, suggesting that the cofactor captured in this structure is not PLP but PMP (pyridoxamine-5'-phosphate), an intermediate in transamination reactions.

PDB reference: human O-phosphoethanol­amine phospho-lyase, 6tor.

References

1. ↑ Vettraino C, Peracchi A, Donini S, Parisini E. Structural characterization of human O-phosphoethanolamine phospho-lyase. Acta Crystallogr F Struct Biol Commun. 2020 Apr 1;76(Pt 4):160-167. doi:, 10.1107/S2053230X20002988. Epub 2020 Apr 1. PMID:32254049 doi:http://dx.doi.org/10.1107/S2053230X20002988